Holiday
by jenny sherman
Summary: COMPLETED - Doctor Weir is ordered by the doctor to take a well-needed break, but unfortunately her break doesn’t do her good at all. And when an old enemy comes to seek her out, she is in real trouble of never making it back to Atlantis


**HOLIDAY**

**Summary:** Doctor Weir is ordered by the doctor to take a well-needed break, but unfortunately her break doesn't do her good at all. And when an old enemy comes to seek her out, she is in real trouble of never making it back to Atlantis

Rating: Violence, torture, hurt, comfort, romance, action, implied sexual situations.

**Chapter 1**

Doctor Weir sat in the briefing room listening to John and Teyla talking about the new trade alliance that they had just successfully negotiated on their recent trip to a planet. Well Elizabeth was trying to listen but she was just so tired that she just couldn't concentrate. They had been on Atlantis now for over 5 months, and after the events of the Huge storm and being held hostage by the Genii, all of her team had, had a chance to recover and take a well earned break, all but her, she knew that she was pushing it as most of her days were now averaging at about 20 hours. She pinched the top of her nose with her fingers to try to relieve the pressure building up in her head.

"So what do you think?" It took her a second to realise that they were talking to her. She looked up and all four faces were staring at her in silence.

"I'm sorry what were you saying?" John frowned and looked at her with concern.

"We were just explaining what we had managed to skilfully acquire on the planet with the Theons". Elizabeth placed her hand flat on the table and looked at them like she was back with it.

"Please continue," she said clearing her throat, had the temp risen much in here or was she having her first hot flush.

"We've finished" John said and immediately regretted it when he saw her embarrassed expression.

"I'm sorry would you all excuse me for a moment" she stood up and realised that all she needed was a breathe of fresh air and that would help her. She headed out of the room.

"What the hell was that all about?" Rodney said in his usual blunt manner.

"She did not appear to be well, she did look rather tired to me" said Teyla trying to defend Elizabeth.

Elizabeth made it out the door and was about to make it out of the control room when she got very light headed. The room began to spin and suddenly she realised that the floor was rushing up to greet her.

"Major, come quickly" shouted one of the technicians as he popped his head into the room.

They all stood up and walked out of the room to find a circle of people staring at something on the floor, when John approached more closely he saw that it was Elizabeth that was drawing their attention.

"Move out of the way, what happened to her" he demanded as he rushed down to her side.

"She just started to sway then collapsed" Said Peter. John wasted no time and picked her up very delicately and headed for Beckets office.

"Doctor we need some help over here" he shouted as he came rushing into the doctors room, Elizabeth was still unconscious in his arms.

"What happened?" asked Carson as John laid her gently onto one of the beds, the sight of her like this was making his stomach churn with worry.

"She just collapsed"

"Okay, step away John and let me work on her" John stepped back and bumped into Rodney. When he looked around he saw that half of the expedition was in the room, all looking just as worried as him.

"Okay everyone, go back to work and I will let you know something as soon as I do" he announced in a tone that showed his gratefulness at their concern.

Rodney, Teyla, Ford and himself stayed behind. They all watched quietly as Carson tested her blood pressure, heart rate and other vitals. After 6 minutes she began to wake. John was instantly by her bedside.

When she opened her eyes she saw a worried John and a busy Doctor Becket fussing around her.

"John, what happened?" she asked, as she looked around confused.

"You collapsed in the control room about 20 minutes ago" John said with such concern that even Carson picked it up. Elizabeth placed her hand on her forehead.

"Why, what's wrong with me?" she asked worried that it would be something serious.

"Elizabeth your tests are all showing me one thing, your exhausted, when was the last time you had more that 6 hours sleep" when she had to think about that answer it was all Becket needed to know. He leant down gently to her side.

"Elizabeth you haven't had a chance to deal with what happened to you when the Genii attacked, that was traumatic enough, but I think that you have been working hard to get everything back to normal" Her eyes lowered at the mention of the Genii attack, he was right she hadn't dealt with the effects of being taken hostage or nearly being shot.

"You leave me no choice Elizabeth, effective immediately you are ordered to take a weeks holiday" Elizabeth looked up at him thinking that he was joking.

"Carson I can't just leave"

"Two weeks" he butted in.

"But I"

"Say another word and I will make it a month, you know that I have the power to relieve you but I would prefer it if you took a volunteer break, now go to the main land, spend some time sunbathing have a swim, do something relaxing because your body is telling you that you need it"

Elizabeth nodded at him and smirked at the look on his face.

"That was all I needed to say to get a word in with you" John said in a mock disgust.

CHAPTER 2 

After a day in the medical room Elizabeth was allowed to leave, she went straight to her room and packed up some clothes and books and then spent 2 hours briefing her 6 replacements.

After saying goodbye to Rodney and Teyla she made her way to the jumper bay and she found John waiting for her, as she knew that he would be.

"Here let me take that for you" he said as he took her bag and stowed it in the jumper for her.

"Thanks" she said as she got inside and sat in the co pilot's chair. John shut the door and sat beside her.

"Ready" he said and she smiled and nodded at him. This was the first time in a long time that they had, had a chance to be alone together.

"Okay, I have two surprises with you today, the first is that we are not going to the mainland" Elizabeth looked over at him with a surprised and excited face on her.

"What, where are" she tried to ask but was cut off.

"tut tut tut, patience" he said as he waved his fingers in the air.

The jumper was positioned in front of the gate.

"All set Rodney"

"Good to go, have a fun time Elizabeth" he said and they went through the gate.

When they came out on the other side Elizabeth's face lit up with excitement and awe. The planet below them was a lot like earth but 10 times more beautiful. John took the jumper up hi into the sky so she could get a good look around.

"What do you think?" he asked in anticipation

"Breathtaking" the smile on her face was enough to keep him going for another year.

"John where are we"

"This is a lovely planet that Teyla told me about called Shalore, they have miles upon miles of sandy beaches with crystal clear water, tropical rainforests, miles of gorgeous stretches of grass and fields, forests, mountain ranges to put ours to shame and snow filled peaks and plateaus, just great for skiing, so what do you fancy first" Elizabeth didn't know where to start.

"John this is truly beautiful, it's just perfect, thank you so much" she leaned over and kissed him gently on the cheek, she didn't mean to it just happened on impulse. She swore that she saw him blush.

After much conversation they decided that the beach was first. John was preparing her second surprise.

Since they had landed, they had both taken a swim, and a sunbath. Then whilst she was snoozing he had pulled out the picnic blanket and loaded all the food on there for them. He moved over to her side gently and stroked her face. God she looked beautiful he though to himself.

"Elizabeth, wake up, time for your second surprise" she woke up and took a moment to gather her surroundings.

"Ta, da" She looked over to where he was pointing and smiled at all the lovely food he had prepared. Roast chicken, bread, salmon, cucumber, cheese, and potatoes, even some crisps.

"How did you, when did you" She couldn't believe that he had done all this for her; she didn't even know that they had most of this stuff in stock.

"Wow, you are truly spoiling me," she said as she sat down realising how hungry she was.

"It is nothing that you don't deserve," he said as he sat down beside her. She smiled at him and they both paused, the moment was perfect as he leaned in close to her, his heart was racing when he realised that she was moving towards him too. There lips touched and they gently kissed, tentatively tasting each other. Then the kiss deepened and his hands were cupping her face and hers were running through his hair. After a while they pulled apart and smiled at each other.

"I have wanted to do that for so long," he said hoping that he hadn't said too much.

"I know exactly what you mean," she said as she stroked his face.

"Seeing you unconscious like that made me realise that I cant wait any longer, I have to tell you how I feel" Elizabeth bit her lip in anticipation.

"I am in love with you" her heart raced, as she knew it was true for her too.

"Oh John, I have been in love with you since the start" They hugged each other then john pointed to the food.

They ate almost all of it laughing and talking as they did. Then they watched the twin suns set on the horizon.

"What a perfect day this has been" he said, after a couple of hours they moved into the jumper and john set up the duvet and temp bed on the floor.

"We are sleeping in here"

"Well I thought it might be cosy and I know for sure that you will be safe"

"What about the villagers, wont they be annoyed that we haven't even said hello yet"

"All taken care of, I came here yesterday and explained the situation and told them that you needed rest, they were only to pleased to let us stay on their world. They said that if we needed anything that we could call on them anytime"

"Such a nice planet and such lovely people, what a rare thing to find in a universe full of evil Wraith"

They sat talking for a while then when Elizabeth yawned for the fifth time, john told her it was time to sleep. They lay down together and he wrapped her up in his arms, she laid her head on his chest and fell off to sleep quickly.

The next day she awoke to find John stroking her hair and staring down at her lovingly.

"Morning" she said as she kissed him.

"Morning" he said returning the kiss, it had taken ever ounce of resolve to stop himself for making love to her last night, but he didn't want to rush this relationship, he wanted this to last forever.

"So what do you want to do today?" he asked. She lifted herself up onto her elbows and thought about it for minute.

"Rock climbing"

"You do rock climbing," he said with a surprise look.

"You seem surprised, I will have you know that I have climbed K2 and many other mountains"

"Okay, your on" The radio crackled in the corned and he stood up and retrieved it.

"Sheppard here"

"Sorry to disturb you sir, but Ford has a situation on P3247X and needs your help" Elizabeth looked up concerned.

"I will be there shortly, give me the coordinate and I will go there from here"

They passed on the coordinates and john put them to memory. Then he said goodbye and turned back to Elizabeth.

"What do you think the situation is, do you want me to come with you, how about"

"Hold on, you are on holiday, I can handle this, please don't worry, I will be gone for a day only. You don't want to tell Carson do you" She looked annoyed at being kept out of the details, she wasn't used to it after being involved so much in the running of Atlantis.

"Okay" she said as she stood up to get changed, John turned his back so she could have some privacy. When she was done he turned back around.

"I will talk to the villagers and tell them where I am going, I have some breakfast here for you, once you have eaten that I will drop you off near the mountains and I will be back for you before it gets too late" she nodded, he knew she was disappointed but he had to go.

"Please be careful," he said kissing her nose gently.

"John, I am an experienced climber I will be fine, I will see you tonight" she moved forward and kissed him.

They ate their breakfast and then he dropped her off at the mountain ranges with some climbing gear and a couple of jumpers just in case she got cold. He returned to the village and asked them to keep an eye on her, as she recently was ill. He decided to fudge the details a little as he was sure that she didn't want them to know all about her history. They agreed that they would send some guides up to the mountain to help her are she needed it.

Now that John was satisfied that she would be okay he left for the planet that Ford was on.

CHAPTER 3 

As Elizabeth watched John fly away she felt alone, they had just found out that they had the same feelings for each other and now he had to leave. But on the very small plus side she felt that she could use a little time to herself, so she decided to look on the bright side and tackle the cliff side.

"Just you and me big boy" she said as she looked up at the red rock. The climb started off easy, there was a long path that led up to the rock face, she took that part nice and slow, admiring the scenery as she went. Finally she reached the red rock surface, it reminded her of the rock and cliffs in the Grand Canyon. She started to climb the rock and as she got a bit higher she started to use her clips and ropes.

"Okay here we go" she said, she attached the Caribbean clips and knocked some of them into the wall then she began to climb higher. After 1 hour and a half she looked down and realised that she was over 100 foot up. The rock surface was tougher than she thought to climb, it was a great challenge and she loved every minute of it.

She noticed that a little bit above her there was a large ridge she made her way to that so that she could have a break. When she climbed onto of it, it was a lovely flat surface the size of a large dinning table. She sat down and looked around at the panoramic view, it truly was breathtaking. After a few moments of admiring the view she decided to climb a bit higher. She could see that the cliff face was about 200 feet above her.

She began to hear a strange rumbling sound; she grabbed onto the side of the rock for support and looked at the little tiny pebbles falling off the side of the cliff.

"Oh shit," she said as she realised quickly what was happening, it was an earthquake and she was in the worst possible place. As the quake and shaking got stronger it got harder to hold on, so Elizabeth thought that the best plan was to make it down to the ridge and stick as close to the rock side as she could, she began to abseil down using her safety rope, unfortunately with the shaking being so strong the pins in the wall that held her so securely, began to shake out of their holes, Elizabeth looked up in time to see one come out and the rope went slack. She felt the sensation of falling and began to panic, but she landed hard on the ridge that was only 20 foot below her.

As she moved she realised that she must have broken a rib, as the pain to breathe and move was substantial. She realised that her only choice now was to sit it out. Finally after another 10 seconds or more it stopped and she knew that she didn't have long before the aftershocks started, she needed to get to the ground and quickly. With great effort she moved her self over the edge and got her feet in a good position, she began to work her way down using her safety rope to swing down a bit at a time.

She looked down and realised that she didn't have far to go now, but then she heard the noise she had been dreading, the aftershock had started. Elizabeth looked up as she heard the clanking of stone and saw large rocks and stones falling down towards her. She pushed herself away from the wall to miss most of them but when she came back to the wall a large bolder hit her ankle and with the shock of it Elizabeth looses her balance and lets go of the rope. Thankfully there was only about 10 foot left and when she realised that she was on the ground she curled up into a ball and covered her head.

After a few more seconds it is all over again. Elizabeth looks at her swollen ankle, shit a broken rib and ankle Carson will not be pleased with me. Using all her strength she tries to stand up.

"Okay standing up I have got but how about the walking part," she says out loud to herself. The tiniest bit of weight on her foot makes her collapse down in pain.

"Okay, down on the bum it is then" Elizabeth manages to slide down the path and only stops when she is sure that she is far enough away from any more falling rocks. Lying back down and taking as many deep breathes as she can with the pain she tries to work out how long it will be before John will be back.

After an hour of sitting in growing pain she hears footsteps and begins to panic.

"Elizabeth" she hears them shouting and realises that it is the villagers.

"I'm over here," she says raising her arms then regretting it instantly as she grabs her side. The men hear her and begin to run to her aid.

"Are you injured, we feared the worst when the quake came as we new that you were climbing, John had asked us to keep a look out for you just in case."

"You are so very kind, I will be fine it is just a broken rib and ankle, I have had worse, how is your village" the men helped her stand and placed her on a makeshift stretcher.

"Oh you don't have to carry me I can try " she started to say but one of the men placed his hand in the air.

"Please, we don't want you injured any more" She smiled at them and let them take her down to the village a few miles away, when they arrived Elizabeth saw that there were not too many injuries, it just looked bad because the huts had been demolished.

"Do not worry, we can rebuild these in a couple of days, we are just fortunate that there were no deaths" They placed the stretcher on the floor and helped her stand.

"We are making a temp area for the injured, I will help you over there" she placed her arm around his neck and started to hope across the courtyard. They heard they familiar sound of the Stargate being activated.

"That must be John, we will get my people to come and help you build your huts"

"You are most kind Elizabeth"

The wormhole flashed open and she waited for the jumper to come flying through but instead to her horror a patrol of 20 Genii soldiers came through.

"Oh shit" she said and the man beside her looked at her worried face.

"Do you know these people"?

"Yes, they are very dangerous, they are killers". At first the commander didn't see her and one of the elders of the village came up to him.

"Welcome to our home, unfortunately we are not in a good position to trade but you are welcome to stay"

"We don't want to trade, we only want one thing Dr Elizabeth Weir, I know that she is here" The elder tried to protect her.

"Whom do you speak of" he lied. The commander placed a gun to his head.

"If you are here Doctor Weir, I suggest that you come forward or I will be forced to execute this man" she new that she had no choice.

"Alright I am here," she said as she moved forward slowly. The commander watched as she hobbled across the courtyard. The commander smiled at her injured state. Finally she stood in front of the Genii.

"Leave them alone" the commander pushed the old man away and shoved the gun towards her chest.

"You look a little worse for wear Doctor" Elizabeth stood as straight as she could as to show no signs of weakness. She wished that John were here. He motioned for her to walk through the gate as they dialled in the Genii home world.

When they reached the other side she was dragged roughly to the underground city, then she was handcuffed and thrown, literally into a cell.

After 10 minutes of trying to calm her self in the quiet darkened cell the door opened and a man entered. Elizabeth's eyes widened as she realised that it was Koyla.

"But I saw you shot, how" Koyla showed her his wound on his chest.

"I am a fast healer, your major Sheppard should have killed me, how is the hero these days" Elizabeth tried to protect him.

"He was killed two weeks ago by a wraith" he looked at her unsure weather or not to believe her.

"What a shame, I was so looking forward to killing him myself, ah well you will have to do," he said as he circled around her.

"What do you want Koyla" she said as she stared forward.

"I want revenge, revenge for killing a whole platoon of men, revenge for shooting me, and revenge for killing my son"

"Your son" she said in surprise. He stood in front of her with hatred in his eyes.

"He was one of the men in the patrol and seeming as I cant get revenge from him I will have to take it out on you instead" and with that he punched her so hard in the ribs that she was certain that he had broken a few more. Elizabeth fell to her knees gasping for breath.

"I don't usual condone this sort of treatment of civilians especially woman, but you're a commander in charge so that makes you military as far as I am concerned. Now tell me, what are the command codes for the computer system at Atlantis, how many military personnel do you have, what is your armoury stock"

"You don't really expect me to tell you all that do you" she said with a smile but regretted it when he punched her hard across the face. She felt her vision fill with stars and she collapsed back onto the floor.

"You will tell me everything I want to know, it is just a matter of how much you want to suffer" and with that he walked out of the door smiling at her weak position.

Elizabeth spat out a mouthful of blood and rolled onto her back. John please help me.

CHAPTER 4 

John felt that Ford could handle the situation on the new planet of P3467G and he decided that it was time to return to Elizabeth. He had managed to pinch some more food from the kitchens to surprise her. She must be hungry now after all that climbing.

He set the coordinates for the planet that Elizabeth was on. He smiled when he came through the gate but his smile faded quickly when he saw the state the village was in.

"Jesus" he set down the jumper quickly and exited before the engines had time to shut off.

"Elder Maxien what has happened" he said as he ran towards him.

"John we had an earthquake" John looked around looking at the injured people.

"My god is everyone okay, do you need help, medical supplies" The elder held up his hand to stop him. John kept looking around at all the poor distressed people.

"John, Elizabeth is gone" John turned around sharply to face him.

"Gone what do you mean gone, gone where, back to Atlantis?"

"No, she was taken by some men, she called them Genti" Johns face turned to horror.

"Genii do you mean Genii" The elder nodded.

"Yes that's what she called them"

"My god" he turned to run back into the jumper.

"Major there is one more thing, Elizabeth is hurt, she fell off the cliff during the earthquake, she has a broken ankle and a broken rib, she is in no condition to be hurt further" Johns heart rate jumper at the news that his dear Elizabeth was hurt so badly and the thought of her in the hands of the Genii just made him sick.

"I will send a team through to help you and some doctors, but I must leave to save her"

"Go, go," said the elder. John rushed back to the jumper and sped back to Atlantis.

"Major what are you doing back so soon," said Pete as he met him in the jumper bay.

"We have a bad situation, Elizabeth has been taken hostage by the Genii and she is in a bad state, we need to assemble a strike team and get in their, and this time I am going to blow those bastards to hell" Whilst the team gathered together and suited up John got as much C4 as he could carry.

He met them all in the briefing room.

"Okay here is the situation, Weir has been taken hostage by the Genii, for what purpose we don't know yet but I am assuming that it is to try to get more C4 or command codes or something that I know she will not give up, so the plan is to fly to the planet close to the Genii home world and fly in, in stealth mode. From there we gain access to the underground facility where we will split into three teams, team one will set the C4 explosive around all key areas and power supplies around the underground, team two will cover them whilst they do this and provide support, team three is with me, we will search for Weir and we will find her, then we will blow that place to kingdom come, any questions"

Everyone in the briefing room had never seen him so determined or angry. Everyone agreed with his plan. Saving Doctor Weir was the most important thing and this time they all agreed that the Genii were not going to get away with it.

"Lets go"

The door opened and Elizabeth looked up through a very swollen eye.

"So the command codes if you please, and the rest of the information I want" Koyla said as he knelt down beside her.

"Go to hell" she spat at him. What happened next was a barrage of blows on her already beaten body.

Once he had finished, he looked down at the bloody woman on the floor.

"You know, there are other methods I have at my disposal, there are a lot of men here who find you quiet desirable, I could let each one of them have an intimate hour with you" Elizabeth dreaded the thought of that and she knew that he would do it.

"Or I could show you what happens when I wet your body with a sponge and then place and electric charge on you, or burn your flesh with a hot poker, do any of these sound appealing to you yet"

"Bring it on you bastard because you will never get anything out of me, I would die before I let you into Atlantis" she could see that Koyla was angry and she was pleased because of that. Truth was she was absolutely terrified, she was just hoping that John would come to save her.

"Fine" he said and walked out slamming the door behind him. Elizabeth lay on the floor crying silently. She didn't know how much longer she could go on.

Sheppard and his team had successfully landed the two jumpers on the Genii home world. They had managed to make it to the barn and only had to take out two Genii. Rodney had insisted on coming along so he could see if there was any technology that they could steal, but truthfully he was just as worried about Elizabeth as John was, she was the only boss that he had, had that he had respected. They reached the hatch and quickly jumped down and John told them to get to work. He and his team searched for Elizabeth and he hoped to god that she was still okay.

The door opened and Elizabeth just looked up from the floor.

"Right then, you did say you didn't care, so lets see what you think when my men have their way with you, but I am the commander so I go first" with that he shut the door and began to undress slowly.

"Benson here sir, all the charges are set, we are making our way back to secure the exit"

"Understood, both teams wait for my order"

"All the charges are set" John said to Rodney.

"So do you want me to undress your are you going to do it yourself"?

She said nothing and just looked away, he smiled at her defiance and ripped open her shirt exposing her bruise and bloody body. He pushed her to the floor and stood looking at her bare chest.

"God you are in a state aren't you, and I am sure that after my men have finished with you, you will be begging to give me the information"

He positioned himself over her and began to kiss her.

"Hey what the hell are you doing here?" shouted out two Genii guards as they came across the strike team. A firefight started and unfortunately the Genii managed to get the alarm raised.

"Sheppard here what's going on?" he said as he stopped after the red lights flashed.

"We have been detected sir, we will hold our position as long as you need"

"Blow the main generator, that should cause some confusion"

"Yes sir"

Koyla was positioned over Elizabeth and was roughly kissing her; he spread her legs and was ready to enter her when the whole base shook. He stopped and looked up as the lights flickered and went out.

"What the hell" he stood up and pulled up his trousers and did up his shirt then left her half naked on the floor.

"Don't go away I will be back" he left her with a guard who was looking at her half naked body with desire.

"Report"

"There is gun fire in one of the tunnels and the main generator seems to have been destroyed."

"What, it must be a rescue team for Weir, gather the men and meet me near the emergency exit.

Koyla came back to the cell to find the guard kissing Elizabeth.

"Sorry, but we don't have time for that now, go to the main tunnel and wait for me" the guard left the room.

"I have been a bit distracted, but I will be back, here have a parting gift" and with that he hit her across the head with his gun, cutting her forehead. He left the cell and ran towards his command centre.

CHAPTER 5 

Finally John made it to the cells with Rodney behind him; there were four guards, which held up no resistance as he managed to kill them all. They used the guard's key to open the cells.

"Jesus John is that Elizabeth" Rodney said as he opened up her cell. John came up behind him and stopped dead in his tracks when they saw her battered, bloody and beaten body. She was awake but dazed; when john knelt down beside her she recoiled back away from him. Rodney took off his jacket and handed it to John to cover up her bare skin.

"Elizabeth, its me, John" he brushed her hair away from her face and wiped the blood away from her eyes. John was seething at the sight of her, her cheeks were blue and swollen, so much so that he could only see one eye, she had a huge gash on her forehead, her body was black and blue too, she had blood in her mouth.

"Jesus"

"John" she said weakly

"Its me Elizabeth, your safe now" he moved to pick her up and she backed away, unsure weather it was him or just a dream.

"Its okay, Beth its me" she looked at him as if she had just really seem him.

"I didn't tell him anything" She tried to smile but her face was too swollen. He slowly moved to pick her up in his arms and this time she let him.

"I knew that you wouldn't"

"It was Koyla" was all she managed to get out and John knew straight away that he was alive and that it was him that did this to her.

He held her close and Rodney could only look on in disgust at the state of her. This is the first time that he had ever wanted to kill someone.

"Team one, I have Weir, blow the whole dam place we are on our way" John carried her as fast and as gently as he could, he could here her grunting with pain every time he moved.

"I'm sorry baby, but we need to get out" he said gently in her ear.

"soookay" she managed to say. Finally with the help of team two they managed to get to the exit. The whole place was in flames and ruined.

"Major, we cant contact Morris or Perry" John heard through his communicator.

"I will just place Weir in the jumper and I will come back to help you"

"Yes sir" John rushed to the jumper and opened the door remotely. He placed Elizabeth on the floor and placed a couple of blankets over her. He left Rodney with her and another guard as he ran back to help his other men.

Koyla had watched Sheppard appear from the invisible ship and go back into the underground city. So he was alive, well there is only one way to get to him now.

John managed to find his men, they were unconscious after being knocked out by the explosions; he and his team members carried them out. The whole place was going to blow and blow big any second. They made it out of the city and headed to the two jumpers. When John approached his jumper he found one guard dead and Rodney unconscious. Elizabeth was nowhere to be seen.

"Rodney, Rodney wake up, what happened where is Elizabeth"

He heard the Stargate being activated and knew what was happening. He ran as fast as he could to it and found himself in a situation that he had been in before. Elizabeth was being held by the throat by Koyla, he had a gun to her head.

"Just like old times hey John" he said as he moved behind her so that John couldn't get a shot in.

"Let her go" Johns said aiming as best he could for his head.

"I don't think so, we had such a good time together didn't we Elizabeth, we even got intimate"

"You son of a bitch" he looked into Elizabeth's eyes and she was giving him the okay to shoot him.

"You killed my son, you killed my men and you shot me, that took a lot to get over, but having Elizabeth here made me have some of my revenge, oh what fun we had" he said as he rubbed his cheek against hers. Elizabeth closed her good eye in disgust.

"So this is where we were last time and what happened then, oh yes you shot me, so this time I think I will change the ending" and with that he moved the gun to her back and shot Elizabeth through the chest. She gasped in shock and fell to the floor. Koyla smiled and jumped through the gate before John could shoot him, he just shot through the wormhole.

Koyla came through the other side closely followed by the barrage of bullets that each hit their target, killing him instantly.

"Elizabeth, Elizabeth can you hear me" the blood was pouring from her chest.

"Ford, I am going to take Weir through the gate she has been shot, please get my men back now"

"Yes sir" John had to wait for the gate to disengage which took a second then he dialled home.

When the wormhole was established he radioed through.

"This is Sheppard, get Becket to the gate room immediately, Elizabeth has been shot I repeat Elizabeth has been shot" he gently picked her up and ran through the gate.

When they got through the other side Beckett was running to meet him.

"Holy Mary" he said when he saw the state of her.

"Jesus john, what have they done to her" John placed her on the gurney and watched as she was wheeled to the infirmary. He looked at himself; her blood was all over him. He knelt down on the floor in front of the gate and just sat there letting it hit him what had just happened.

2 hours later

Rodney was fine now and everyone was back at Atlantis, John was in shock at the state his beautiful Elizabeth was in. He couldn't believe that anyone could do this to such a gentle and caring person. Carson had operated on her immediately it has taken only 30 minuets to get out the bullet and fix her lung and small internal bleeding. He had set her ankle in a cast and stitched her forehead. She was in intensive care now and in an induced coma.

Finally Carson came out to see John, Rodney, Ford and Teyla who had not moved from the waiting room. John stood when he saw him coming in.

"Well guys its like this, she is in a very serious state" he said as he took off his scrubs.

"What did he do to her?" Rodney asked.

"God where do I start, she has a broken ankle that I have reset and plastered, she has a severely bruised kneecap, she has four broken ribs, severely bruised chest, small internal bleeding around her stomach, her shoulder and her cheek bone are both cracked. She has a nasty gash on her forehead that has taken 12 stitches to heal, and she has a fractured skull, not to mention the bullet wound that missed her heart by only an inch, that is giving me cause for concern more than the rest of her injuries, because of all this trauma her body has been through I have had to induce a coma to let her body heal"

They all sat there in silence, stunned at the extent of her injuries. John looked completely lost and Carson could see that he was still in shock.

"Do you want to see her John" he nodded and move forward followed by the rest of them.

"Sorry guys, but just one at a time" Carson led john through to the ICU. He stood frozen at the sight of her.

"Doc, Koyla mentioned that they had been intimate, have you checked her for signs of rape" Beckett looked at him in disgust.

"I can't believe that on top of her injuries, that they would subject her to that, give me a minute and I will check that"

"Will she survive this Carson" John asked quietly

"She is such a strong woman, I am surprised that she survived the bullet wound, that alone tells me that she will survive her injuries, but the mental state is something different, she has suffered severe mental torture, you will have to make sure that you are there for her throughout this John" John looked at him with tears in his eyes.

"You know I will be"

Carson pulled around the curtain and asked for a female nurse to assist him. He found no signs of rape but there was bruising around her legs as though she struggled to stop them spreading her legs, but he was pleased to find that they hadn't finished the job.

He pulled back the curtain and walked over to John who held his breathe.

"She hasn't been raped but I think that they tried to, I think that you arrived at the perfect time, any longer and she would have been" John let out a breath.

He sat down beside her bed and looked at her face. He took her hand and just sat there in silence.

CHAPTER 6 

It had taken 4 days before Carson felt that it was okay to bring her out of the coma.

Another 2 weeks and she was able to mumble in her sleep. Every day John had been there, weather she was awake or not. When she finally opened her eyes she wasn't surprised to see him sitting there.

"John" she said as she looked at his tired and unshaven face.

"Doc she's awake" he shouted as he turned his attention back to her, he grabbed her hands and kissed them.

"You look awful," she said to him

"How long have you been sitting there"

"Everyday, just in case you woke up and needed me, how do you feel"

"Like I had the crap beaten out of me," she said with a fake smile.

"We don't need to talk about anything until you are ready" she nodded and then he saw the tears brimming in her eyes, they spilled over and ran down the side of her face.

"It was awful"

"I cant imagine what you went through, but I can tell you that every military man in this base has doubled or tripled their respect for you, a lesser man would have given in under that sort of torture, god I am so proud of you"

"Elizabeth, how are you feeling" Carson came over and checked her pupils and heart rate.

"Not so good Carson, what state am I in" Carson explained the state of her injuries and Elizabeth couldn't control the tears that fell.

Every one had come to visit her one at a time, no one had asked about what happened they knew that when she was ready she would talk.

She spent a month in the infirmary, finally John convinced Carson to let her back to her quarters and he agreed as long as he would look after her.

Her cast was due to come off her ankle in the next couple of days; she could walk around now without her sticks. John had not told her that she could leave and just helped her into a chair one morning.

"Where are we going"?

"Come on, we are breaking out" he said with a smile she laughed for the first time since this ordeal began as he sped past the doctor and his nurses. Carson of course knew what was going on but he let John carry on.

"Close your eyes" he said as he waited outside her quarters. She did as he asked, as she knew that she felt safe with him. He pushed her wheelchair inside and to her bathroom. He had, had some friends of Teyla's make Elizabeth a bath; an extra special deep bath and Rodney had offered his time to put in a whirlpool system.

"Okay open your eyes" when she did, she gasped with surprise. In the middle of her bathroom was a large beautiful bath with buttons down the side, a table attached for drinks and a foot stool at the end of the bath so she could lie down and relax, the whole room had been filled with candles.

"Oh John" she said. She reached out her hand and grabbed his.

"Thank you" he leant down and kissed her lightly, he had been very cautious about being too overfriendly with her after what she had been through, he just wanted to go at her pace.

"Shame I can't have a bath" she said pointing at her case.

"Well actually" he said and then moved away to her front door. Carson was waiting with the saw to cut off the cast. She laughed at the two's devious plan.

"You two" After he had cut off her cast he left with a smirk at John.

"Now how about that bath" he said as he filled it up with lovely hot water.

"An added feature compliments of Rodney" he said, he pointed to the buttons on the side and pushed one. The jets jumped into action and the still water became a lovely whirlpool bath.

"Remind me to give him a big kiss and hug"

"Well I did help design it and it was my idea, so do I get a kiss too" she pulled him down and kissed him fiercely. After she pulled away she caught him blush.

"Wow" he said

"Okay, I will let you have your bath and I will be here when you come out" he said and began to leave to give her some privacy.

"Um, John, I cant reach my back and I don't want to be on my own, would you join me" John raised his eyebrows.

"In the bath" she nodded.

"If your sure that your okay with that" she nodded and he felt that he should turn away whilst she got undressed.

"It's okay John I am safe with you and I trust you" so they undressed at the same time, John had to think of all the boring things in the world otherwise she might just see how much he was aroused by her naked form.

She got in first and John got in behind her, she passed him the soap and he began to wash her back. She relaxed back against his chest when he had finished.

She felt like it was time to tell someone what had happened, she knew she was ready to tell him.

"I thought that you would be mad with me when I fell off that cliff, as those kind men carried me back to the village all I could think of was how angry you would be with yourself for letting me get hurt" he sensed that she wanted to talk so he kept quiet and just listened.

"When the Stargate opened I thought it was you and I was so excited, but when I saw those men run through with guns and those uniforms, I knew, I knew that they had come for me. I wasn't going to show myself but they threatened to kill one of the elders if I didn't so what choice did I have".

He kept rubbing her shoulders and she was grateful that he didn't interrupt.

"We got to the Genii home world and they threw me into a cell and handcuffed me, then" she paused and wiped a tear away from her face.

"Then he came in, I was stunned that he was alive I was so sure that you had killed him. He hit me so hard in the ribs that I actually felt the ribs cracking; he told me that he wanted revenge for killing his men; his son, his wound and he wanted you. I tried to protect you so I told him that you had been killed by the wraith and he seemed to believe me, he told me that he would take the revenge out on me as he saw me as military leader not a civilian."

She paused for a moment and then wiped more tears away.

"He wanted command codes, and information about Atlantis and I told him to go to hell, then he, he punched me across the face and smiled as he left the room, I remember the taste of blood, it was so metallic, I had to spit it out on the floor" she unconsciously rubbed her cheek as if remembering the pain.

"I knew then that he would kill me if needed, all I could think of was you. He left me for a while and then he came back and asked me again for the information, I said something else to him I cant remember kind of like drop dead or something like that then I just remember the pain as blow after blow came from him. Then he said" she stopped and John thought he should say something.

"Its okay, you can tell me" she nodded and carried on.

"He said that he would let his men each have an hour with me, and I knew that he meant it. I told him to bring it on, he seemed pleased with my defiance but I was terrified" her tears were flowing freely now and it was breaking Johns heart to listen to what she had been through alone.

"Eventually he came back and told me that he was going to let his men have there way but he was there commander and he was entitled to go first and then he" she started to cry and sob.

"He began to undress himself, and he ripped off my clothes and began to kiss me, I knew that there was nothing I could do, he began to kiss my body and I began to struggle, he tried to spread my legs and I began to fight, I realised that I was going to fight with every ounce I had"

He shoulders were shaking in fact her whole body was as she cried and sobbed louder.

"He was about to enter me when the first explosion rocked the cell, he stopped and got dressed and left me, but the guard he left decided to have a go and he put his fingers inside me and" at that point she stopped and cried and cried. John held her tight and let her cry as long as she needed. He couldn't believe that she had been through so much.

"I remember being in the jumper then Rodney yelling in pain, then being in front of the Stargate then the pain I my chest, like heartburn a thousand times stronger" she kept crying and he hugged her tightly.

After 40 minutes of crying she began to calm down, in fact when john looked he realised that she had cried herself to sleep. He slowly picked her up and carried her to the bedroom. He wrapped at towel over her and then placed her covers on top of her and kissed her forehead. When she was asleep she had no worry lines on her face, she looked like she had a care in the world. John knew that it would take a long time before she would get over this, but she had made the first step by talking about it.

In the coming months they discovered that a Genii spy was on the planet that Elizabeth was holidaying on. In fact they had spies on many worlds. They had also learnt the Koyla had indeed been killed by John after he got through the Stargate, that had made Elizabeth feel much better. The genii home world had suffered a large wraith attack since their underground facilities had been exposed due to the explosions. Elizabeth had been in therapy since the day after she talked to John. Her injuries had all healed and she only had a few permanent scars left.

Nobody in the city had seen her as any less of a commander after what she had been through, in fact they had all seemed to have had more or a respect for her now then ever. She and John had been seeing each other and John was happy to let them carry on at her pace. Finally she was secure, safe and happy again.

THE END 


End file.
